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Journal of Caribbean Amerindian His ton- and Anthropology 

KACIKE: Journal of Caribbean Amerindian History and Anthropology ISSN 1562-5028 
Special Issue edited by Lynne Guitar 

The Use of Mitochondrial DNA to Discover Pre-Columbian 
Migrations to the Caribbean: Results for Puerto Rico and 
Expectations for the Dominican Republic 

Dr. Juan C. Martinez Cruzado 

In this study, we use 
Mitochrondrial DNA technology (mtDNA) 
to improve our understanding of the pre- 
Columbian migrations to the Antilles that 
gave rise to the Tainos. As a basis for 
our work, we need to review various 
studies, principally of the archaeological 
type, that have given us knowledge of the 
pre-Columbian migrations to the Greater 

It is known that more than 8,000 
years ago the Greater Antilles were 
inhabited by nomads who depended for 
their survival upon the foods that they 
could collect and the animals that they 
could hunt. That era is known as the 
Lithic Era, which is distinguished by the 
stone tools that these people made. 

Some 4,000 years later, we begin 
to note a great quantity of tools and 
adornments made of shells and some 
made of bone. That era is known as the 
Archaic Era, populated by nomads who 
appear to have subsisted principally on 
seafoods, but who also ate terrestrial 
products. It was not until some 2,200 
years ago that a ceramic culture arrived 

in the Greater Antilles, consisting of 
agriculturalists who built permanent 
settlements near their areas of cultivation. 

Little is known about the 
migrations from which the nomads 
originated, better known as the pre- 
ceramic culture. Three routes have been 
identified by which there could have been 
migratory waves to the Greater Antilles: 
proceeding from the Florida Peninsula by 
means of Cuba, proceeding from the 
Yucatan Peninsula also by means of 
Cuba, and proceeding from the Orinoco 
Delta by means of the Lesser Antilles. 
Dental studies done by Dr. Edwin Crespo, 
as in other studies, suggest that there 
were at least two migratory waves to the 
Greater Antilles. For this reason, 
confirmation of the use of the routes does 
not necessarily indicate that the other 
routes were not also used. 

Distinct ceramic cultures existed in 
the Greater Antilles. Even before the 
time of Christ, on the island of Vieques, 
there already existed a Huecoid culture 
and Saladoid culture, clearly 
distinguishable by their ceramics, but also 

Dr. Juan C. Martinez Cruzado - The Use of Mitochondrial DNA 

through other cultural aspects. For 
example, while the burials of the 
Saladoids can be found relatively easily, 
the remains of Huecoid bones have never 
been found. All that has been found is 
one milk tooth. For this reason, it is 
believed that the religions of both cultures 
could have contained very different 
elements. Furthermore the Huecoids 
were specialists in working with semi- 
precious stones, which they frequently 
sculpted in the form of animals. Among 
them the figure of a bird stands out that 
many have identified as the Andean 
condor, for which reason they attach a 
continental origin to this region. Deposits 
with ceramic elements very similar to 
those of the Huecoids have been found 
near the mouth of the Guapo River in 
Venezuela. From there they would have 
taken the maritime route eastward toward 
Puerto Rico, Vieques, and other islands 
in the Northeastern Caribbean. The 
Saladoids, on the other hand, migrated 
from the region of Saladero near the 
mouth of the Orinoco River by means of 
the Lesser Antilles until they arrived in the 
Greater Antilles. 

The Huecoid culture lasted some 
few hundred years, but the Saladoid 
culture, evolving with time, lasted until 
approximately the year A.D. 600. Certain 
evidence has been found in Puerto Rico 
that suggests great, natural events of a 
catastrophic nature that could have put 
an end to the Saladoid culture. What is 
certain is that a clearly distinct culture 
developed beginning from that date, the 
Ostionoid, which is divided into two 
stages known as pre-Taino and Taino. 
We do not know if the Ostionoid culture 
represents a marked cultural change of 
the Saladoid culture people due to the 
natural catastrophic events or some other 
type of event, or if it represents the arrival 

of a new migratory wave of 
Southamerican origin. 

In conclusion, the archaeological 
evidence can identify four pre-Columbian 
migrations to the Greater Antilles: two 
pre-ceramic and two ceramic. The actual 
number of pre-Columbian migrations very 
well might have been only four, but there 
could have been many more. 

We will see now what the mtDNA 
that we can extract from the 
contemporary inhabitants of the Major 
Antilles could offer us. The vast majority 
of our genetic material, perhaps better 
known as DNA, is found in the nucleus of 
the cell. The mtDNA, however, is not 
located in the nucleus of the cell but in an 
organelle known as the mitochondria. 
While nuclear DNA is inherited in equal 
parts from one's father and mother, 
mtDNA is inherited only from one's 
mother. It does not mix with that of the 
father and for that reason remains intact 
generation after generation, thus 
maintaining its original identity. That is to 
say, despite the intensive mestizaje 
(genetic "mixture") that has characterized 
our region over the centuries, we 
Caribbeans have mtDNAs that have 
maintained their original identity and that 
can be identified as African, Indian, or 
Caucasian. Their identity depends upon 
the women in our genetic tree at the end 
of the strictly maternal ancestral line. If 
this great-great-great grandmother were 
indigenous, then the corresponding 
Caribbean would have an indigenous 
mtDNA. He or she would have inherited 
it intact from that great-great-great 
grandmother who lived through those 
terrible first years of the colonization by 
means of his or her great-great 
grandmothers, great grandmothers, and 
maternal grandmother. 

It was only a few months ago that 
we concluded a study of the ancestral 

© 2002, Juan C. Martinez Cruzado 
KACIKE: The Journal of Caribbean Amerindian History and Anthropology 
ISSN 1562-5028 - 

Dr. Juan C. Martinez Cruzado - The Use of Mitochondrial DNA 

inheritance, through the strictly maternal 
line, of Puerto Ricans. Using the 
population information from the 1990 
Census as well as a computer model, we 
randomly chose 1,067 residences in 
order to match the population density 
across Puerto Rico; therefore, these 
residences constituted a genuine 
representative sample of all of Puerto 
Rico's residences. Equally, one adult 
within each one of these residences that 
was inhabited was randomly chosen to 
guarantee the representation of our 
sample. Of those 1,067 residences, 985 
were inhabited. Of the 985 inhabited 
residences, we could contact a selected 
adult in 875 of them. In exactly 800 of 
these 875 cases, the adults agreed to 
give us some samples of their hair roots 
in order to study their mtDNA. That is to 
say, 800 of the 985 selected adults 
(81.2%) participated in the study, and we 
could be satisfied that the 800 
participants constituted a representative 
sample of the Puerto Rican population. 
Of the 800 participants, 489 (61.1%) had 
mtDNA of indigenous origin, 211 (26.4%) 
had mtDNA of African origin south of the 
Sahara, and exactly 100 (12.5%) had 
mtDNA of Caucasian origin. 

There are two important things that 
have to be recalculated, confronted with 
these results. First, because inheritance 
is only through the mother, the mtDNA 
only traces the migrations of women. 
These results imply that there have been 
few migrations of women to Puerto Rico 
in post-Columbian times relative to the 
quantity of local women in the country, 
and that the cumulative effect of all those 
migrations after 500 years of colonial 
history has been to reduce the 
percentage of indigenous mtDNA from 
100% to 61%. 

Second, it is certain that the 
historical documentation reveals multiple 

occasions in which Indians from the 
Yucatan, from Hispaniola, from Margarita 
Island, from Brazil, and from other 
Spanish and Portuguese colonies were 
brought as slaves to Puerto Rico. 
Nonetheless, the historical documentation 
also reveals that the importation of 
African slaves greatly exceeded the 
importation of Indian slaves. Therefore, 
the greater frequency of indigenous 
mtDNA in Puerto Rico can only be 
explained from the basis of the mtDNA of 
Native Puerto Ricans, from whom must 
have come the major part of the 
indigenous mtDNA present in the country. 

Although hair roots do not always 
provide sufficient material to make 
studies in great detail, many of the 489 
samples that ended up being of 
indigenous origin had the necessary 
quality to let us study them more 
profoundly and to generate a hypothetical 
schematic of the pre-Columbian 
migrations to Puerto Rico. Owing to the 
affinity that existed between the Tainos of 
Quisqueya and those of Boriquen, we 
believe that this hypothetical schematic of 
the pre-Columbian migrations ought to 
apply in good measure to the Dominican 

In order to better understand these 
detailed studies, it is necessary to know 
certain things in the field of molecular 
genetics and mtDNA. The molecule of 
mtDNA is the only DNA molecule in our 
cells that is circular. Also, it is the 
smallest. It was sequenced in its totality 
in Great Britain in 1981, determining that 
there were 16,569 long nucleotides. For 
those less expert in DNA, we can imagine 
the mtDNA molecule like a necklace of 
16,569 pearls. Each pearl has a number 
and they are strung in order from 1 
through 16,569. Furthermore, each pearl 
has a letter that could be A, T, C, or G, 
depending upon what its nitrogen base is. 

© 2002, Juan C. Martinez Cruzado 
KACIKE: The Journal of Caribbean Amerindian History and Anthropology 
ISSN 1562-5028 - 

Dr. Juan C. Martinez Cruzado - The Use of Mitochondrial DNA 

The change of one letter for another is 
known as a mutation. 

Usually, the detection of mutations 
in the mtDNA is done by means of proof 
of restriction. An endonuclease 

restriction is an enzyme that selectively 
directs the DNA in a specific sequence. 
For example, the endonuclease Alu\ cuts 
the DNA uniquely at those points where 
the DNA has sequential AGCT. If it were 
a molecule that had the AGCT sequence 
at some point, that molecule would be cut 
into two fragments by the endonuclease 
Alu\. If a mutation were to occur in one of 
the four nucleotides that form the 
sequence, the sequence would cease to 
exist, and Alu\ would leave the molecule 
intact. This example illustrates one 
mutation that eliminates a restriction site 
known through the endonuclease. Other 
mutations create them. There are distinct 
restriction endonucleases that allow us to 
detect mutations easily at many points of 
the mtDNA. Thus, the mutations can be 
identified citing the number of the pearl 
where the mutation occurred in 
conjunction with the effect of the mutation 
due to the elimination or creation of a new 
restriction site. 

Usually we think of a mutation as 
something very bad that has produced a 
clearly visible change and is unfavorable 
in the person, like producing a third eye 
or leaving him without a leg, but recently 
it has been demonstrated that the great 
majority of mutations do not produce a 
clearly visible effect in a person. Each 
one of us has approximately 175 
mutations in the nucleus and nonetheless 
we consider ourselves normal. Well then, 
mtDNA is so small that a mutation occurs 
in it only once every 3,000 years. These 
mutations permit us to track the human 
migrations that have occurred throughout 
the world since human beings arose in 
Africa some 150,000 years ago. 

Frequently, migrations to unpopulated 
places have been accompanied by 
mutations. This causes the derived 
populations to have certain mutations that 
distinguish them from the original 
population. The mtDNA that composes a 
mutation that arose in an ancestral 
woman who has them in common with 
others, forms a family of mtDNAs known 
as a haplogroup. The mutation that all 
the mtDNAs have in common is known as 
the marker of the haplogroup. All of the 
mtDNAs that belong to a haplogroup 
have the marker of the haplogroup. 
Clearly, measured across the passage of 
time, there are some mtDNAs that belong 
to a haplogroup that develop particular 
mutations. It is said that two mtDNAs that 
belong to the same haplogroup but that 
are distinguished one from the other by 
additional mutations at some point of the 
molecule belong to distinct haplotypes. 

The majority of the indigenous 
mtDNAs have Asian origins. Some 
25,000 to 30,000 years ago, a group of 
Siberians crossed the Bearing Sttrait; 
thus human beings entered the New 
World for the first time. Among them 
were women who carried mtDNAs that 
belonged to the Asiatic haplogroups A, C, 
and D. It is possible that, by an 
alternative route closer to the sea, a 
haplogroup B simultaneously entered the 
New World, a group that was also Asiatic, 
but which is not found today in Siberia 
like haplogroups A, C, and D. Today, and 
possibly also in the past, haplogroup B is 
common from Central China through the 
Southeast in Indonesia, Polynesia, and 
Micronesia. A fifth indigenous 

haplogroup is haploid X. This is not 
found today in Asia, but in Europe, and 
could represent an independent migration 
from Europe via Greenland to the New 
World. Today within the New World, the 

© 2002, Juan C. Martinez Cruzado 
KACIKE: The Journal of Caribbean Amerindian History and Anthropology 
ISSN 1562-5028 - 

Dr. Juan C. Martinez Cruzado - The Use of Mitochondrial DNA 

haplogroup X is found only in North 

The indigenous haplogroups and 
their markers, those mutations that 
characterize the haplogroups, are: for 
haplogroup A, +665 Hae\\\, which is a 
mutation that creates a site of restriction 
known through the nuclease Hae\\\ in 
pearl number 663; for haplogroup C, 
+13,262 Alu\; for goup D, -5,176 Alu\, 
which is a mutation that eliminates a site 
of restriction in the pearl number 5,176; 
and for haplogroup X, +14,465 Acc\. The 
marker of the haplogroup B is the only 
one that does not consist of a change of 
restriction. It consists of a deletion of 
nine pearls beginning in position 8,272, in 
a region of the mtDNA molecule known 
as region V. 

The distribution of these five 
haplogroups in Puerto Rico was the 
following: Of the 489 samples of 
indigenous origin, 255 (52.!%) belonged 
to haplogroup A, 175 (35.8%) to 
haplogroup C, 42 (8.6%) to haplogroup B, 
17 (3.5%) to haplogroup D, and zero to 
haplogroup X. This distribution structured 
around two haplogroups, specifically 
haplogroups A and C, which constitutes 
88% of the indigenous samples, is typical 
of the New World tribes. It is additional 
evidence that the majority of the mtDNAs 
of indigenous origin in Puerto Rico 
originated from only one tribe that could 
not have been any other than the local 
tribe, the Tainos, because if it were 
otherwise we would have seen a 
distribution that was more equally 
structured, with all the haplogroups 
represented in comparable frequencies. 

We conclude that the great 
majority of the Tainos of Puerto Rico 
belonged to the haplogroups A and C. 
We proceed now to explore the distinct 
migratory routes that could have given 
origin to the Tainos. 

Studies made of other tribes on the 
continent show a clear dichotomy 
between the Indians who occupy the 
region from the north of Venezuela 
through the Amazon to Patagonia and the 
Indians who occupy the region to the 
west of the Andes, Central America, and 
North America. According to the theory 
of the Bering Strait, the settlements of 
human beings in the New World spread 
from north to south. Using this 
schematic, we can visualize the 
Columbian Andes as a great obstacle to 
the total occupation of South America on 
the part of the Indians who arrived from 
Central America. Few of the Indians 
would have crossed the Andes when it 
meant crossing them to enter the Amazon 
jungle. In biological evolution, this type of 
event is known as a founding event. 
Founding events are characterized by 
being susceptible to a genetic drift. 
Genetic drift increases the likelihood of a 
dramatic change in the frequency of 
haplogroups of a population that could 
occur fortuitously when the size of the 
population is dramatically reduced. The 
reduction in size of the population that 
crossed the Andes could have affected 
the frequency of the haplogroups of that 
population. As a consequence, while the 
populations west of the Andes have 
haplogroup A as the most frequent and 
haplogroup D as the least frequent, from 
Venezuela to Patagonia, haplogroup A is 
the least frequent and haplogroup D the 
second most frequent after haplogroup C. 
The frequencies of haplogroups from the 
Florida peninsula, Mexico, and Central 
America are very similar in that 
haplogroup A is the most frequent and D 
the least frequent. They differ only a little 
in that haplogroup C is a little more 

Accepting that the Saladoid culture 
as well as the Huecoid had a 

© 2002, Juan C. Martinez Cruzado 
KACIKE: The Journal of Caribbean Amerindian History and Anthropology 
ISSN 1562-5028 - 

Dr. Juan C. Martinez Cruzado - The Use of Mitochondrial DNA 

Southamerican origin, the present 
schematic has two explanations. One is 
a new genetic drift. The maritime route 
along the Greater Antilles could have 
been accompanied by a marked 
reduction in the size of the population, 
occasioning anew a drastic change in the 
frequency of the haplogroups of the 
population and producing one more 
similar to that of North and Central 
America than that of the original 
population in Venezuela. The second 
explanation is based on the principle in 
the field of population genetics that says 
that when a migratory population arrives 
at a place where there already exists 
another population and competes against 
it, the genetics of the native population 
will remain predominant. Based on this 
schematic, the predominant haplogroup, 
A, would belong to the original population 
of Puerto Rico, the pre-ceramic 
population, which very well might have 
originated on the Yucatan Peninsula or 
that of Florida. The less frequent 
haplogroup, C, would belong to the 
people of the ceramic culture who arrived 
later from Venezuela. That is to say, the 
Tainos would have been the product of a 
mixture between at least two ancestral 
indigenous cultures. The evidence that I 
am showing you suggests that the 
second explanation is the most probable. 

All haplogroups can be divided into 
two subgroups according to the presence 
or absence of a site of Hae\\\ restriction in 
position 16,517. This site of restriction is 
hypermutable, which means it has little 
filogenetic value. Nonetheless, its 
filogenetic value ought to be greater for 
the human migrations in the New World 
due to the recentness of those 

Haplogroup A can be divided into 
groups A1 and A2 according to the 
presence or absence of the site of Hae\\\ 

restriction in position 16,517, respectively. 
The proportion of A1 above A2 in Puerto 
Rico is practically identical to that of 
Florida, like that of Mexico and Central 
America, and is distinct from that of the 
Amazon. The theory of genetic drift by 
means of the Greater Antilles would have 
to come up with an explanation not only 
for the distancing of the frequency of 
groups from the Amazon, but also for the 
chance approximation to the frequency of 
groups to that of the frequency found in 
Florida and in Mexico-Central America. 

In contrast, a similar analysis of 
haplogroup C does not reveal any 
tendency. Puerto Rico is the only place 
of all the studies where group C1 is more 
frequent than group C2. 

We decided, then, to study 
haplogroup C more closely. We took as a 
point of departure the extensive studies 
that have been conducted at the 
laboratory of Doug Wallace at Emory 
University in Atlanta. There, the mtDNA 
molecule has been completely analyzed 
for 14 nucleases of restriction in 338 
Amerindians who belong to 21 New 
World tribes. These 338 Amerindians 
included 64 with mtDNA from haplogroup 
C. Upon doing the analysis of the 64 
from haplogroup C, 25 distinct mtDNAs 
could be observed known as haplotypes. 
Of these 25 haplotypes, 21 are private, 
that it to say, they are encountered in only 
one of the 21 tribes; two haplotypes are 
semi-private, being encountered in only 
two Amazonian tribes; and two 
haplotypes are cosmopolitan. These last 
are AM32, which is found in seven tribes 
in North, Central, and South America, and 
AM43, which is found in four tribes in 
North, Central, and South America. The 
only difference between AM32 and AM43 
is in the Hae\\\ position 16,517, by which 
it is theorized that AM32 was the only 
haplotype from haplogroup C that 

© 2002, Juan C. Martinez Cruzado 
KACIKE: The Journal of Caribbean Amerindian History and Anthropology 
ISSN 1562-5028 - 

Dr. Juan C. Martinez Cruzado - The Use of Mitochondrial DNA 

crossed the Bering Strait. A little later, 
the hypermutability of the Hae\\\ 16,517 
site permitted the generation of haplotype 
AM43 before more stable mutations 
arose. When the more stable mutations 
arose, the tribes were already formed, 
and social restrictions imposed upon 
intertribal marriage limited the haplotypes 
generated by the stable mutations to one, 
or a few, nearby tribes. Thus, the new 
haplotypes remained private or semi- 

With this background in mind, our 
goal was to analyze the mtDNA of 79 
Puerto Ricans who belonged to 
haplogroup C for the 17 sites of restriction 
in which Dr. Wallace's laboratory had 
found variability, as well as the 16,517 
Hae\\\ site, with the hope that some 
private haplotype would arise that would 
let us precisely locate the tribe's origin. 
We found only one additional variable site 
of restriction, in 7,013 Rsa\. We then 
proceeded to analyze the rest of the 96 
mtDNAs of haplotype C that we had 
found for these two sites of restriction and 
we ended up with only three haplotypes. 
These were 104 (59.4%) AM79, 67 
(38.3%) AM32, and four (2.3%) AM43. 
AM32 and AM43 are the haplotypes of 
the founders of the New World that are 
found as often in North as in Central and 
South America, which means we could 
not precisely locate their precedence. 
Not so for AM79. AM79 has only been 
found in two Amazon tribes, the 
Yanomamos and tie Crajos. Until our 
study, they had not been found any other 
site in the world; therefore their presence 
in Puerto Rico brought us to fearfully 
conclude that we had erred about the 
majority of Puerto Rico's haplogroup C 
having an Amazonian origin. Where did 
AM32 and AM43 come from? We don't 
know. But the evidence leads me to 

suggest to you that they arrived in Puerto 
Rico long before AM79. 

All mtDNA can be divided into two 
regions: a region codified where all its 
genes are found and that measures 
15,447 nucleotides long and a region with 
genes some 1,122 nucleotides long. 
Within the region with genes, we have 
two hypervariable regions of between 300 
and 400 nucleotides each, whose 
sequences can provide us with very 
valuable information if we analyze them 
using the method of median networks. In 
this method, the haplotypes that arise in 
the sequences are represented by circles 
of proportional size to the frequency 
within the population that they represent. 
The circles or haplotypes are 
interconnected, and the relationship 
between one haplotype and another is 
represented with cross-connecting lines 
below the connections among the circles. 
Each cross-connecting line represents a 
mutation between one haplotype and 

We sequenced both hypervariable 
regions in 35 samples of haplogroup C, 
21 of which belonged to AM79 and 14 to 
AM32. The differences are dramatic due 
to the production of haplotypes in the 
sequence and due to their distribution. 
The 21 samples of AM79 produce only 
four haplotypes, while the 14 AM32 
produce seven. In AM79 we have a 
haplotype that represents 18 samples. 
From this haplotype arose the other three 
haplotypes of AM79, each one 
representing a single sample. In contrast, 
AM32 can be divided into two groups: 
one of them consists of eight samples 
represented in the six haplotypes, and the 
other consists of six samples represented 
by only one haplotype that is separated 
from the nearest haplotype by seven 

© 2002, Juan C. Martinez Cruzado 
KACIKE: The Journal of Caribbean Amerindian History and Anthropology 
ISSN 1562-5028 - 

Dr. Juan C. Martinez Cruzado - The Use of Mitochondrial DNA 

The interpretation is the following. 
The simplicity of AM79 suggests a recent 
migration, or at least it did not occur far 
enough back in time to accumulate the 
mutations that produce a complete 
median network. Furthermore, the 
haplotype's location within the median 
network that represents the 18 samples 
connecting itself to the other three 
haplotypes of AM79 suggests that it is the 
founder haplotype of AM79. Moreover, 
its very high frequency suggests a rapid 
population expansion, like that which we 
could expect of an agrarian and ceramic 
culture that exploits the resources at its 
disposition more efficiently than archaic 

AM32 is itself divided into two 
groups. One of them consists of one sole 
haplotype that represents six samples. 
This ought to correspond to a recent 
haplotype, but does not account for 
derivative haplotypes. Possibly it co- 
migrated with AM79 from South America, 
or perhaps it represents an even more 
recent migration. In contrast, the second 
group of AM32 presents a complete 
median network that includes six 
haplotypes representing only eight 
samples. The six haplotypes are 
differentiated one from another by one 
sole mutation; furthermore, there is none 
that occupies a clearly defined central 
position as is the case with AM79. This is 
a manifestation of an ancient group that 
could not achieve a population expansion 
over a long time period, which 
occasioned the accumulation of distinct 
haplotypes without the founder achieving 
such high frequencies. By the complexity 
of the group, this last group seems to 
belong to an ancient pre-ceramic group, 
almost as old as those of the haplogroup 
A that we will see as we continue. 

Dr. Wallace's laboratory studied 
the complete mtDNA molecule for 120 

Amerindians of haplogroup A in 21 tribes 
with 14 endonucleases of restriction. 
They generated 35 haplotypes, 30 of 
which were private and three semi- 
private. Only two were cosmopolitan: 
AM1 is found in nine tribes from North, 
Central, and South America, while AM9 is 
found in seven tribes in the same three 
large geographic regions. Again, the only 
difference found between AM1 and AM9 
falls into the 16,517 Hae\\\ position, 
hence the theory of there being only one 
founder group that crossed the Bering 
Strait and brought haplogroup C, could 
also apply for haplogroup A. We 
proceeded the same as we did for 
haplogroup C with the hope of 
discovering some private or semi-private 
haplotype that could help us to precisely 
locate the origin of those mtDNAs of 
haplogroup A. We analyzed 53 samples 
of haplogroup A for all the 21 sites of 
restriction for which Wallace's laboratory 
found variables in the mtDNAs of this 
haplogroup. Unfortunately, we only found 
two cosmopolitan haplotypes, AM1 and 
AM9, hence we could not precisely locate 
its origin. 

We then proceeded to sequence 
the hypervariable regions within the 
region of the mtDNA that lacks genes. 
This was done in 42 samples of 
haplogroup A. The results produced two 
principal groups. The first group 
composes the most complete median 
network that we have had, which 
suggests that it represents the oldest 
migratory wave. It has two haplotypes 
that are very similar to each other; they 
are differentiated by one sole mutation 
that occupies central positions, like 
founder haplotypes. Both originate 
similar complex networks, which suggests 
that the two founder haplotypes belong to 
the same migratory wave. One of the 
founder haplotypes seems to have 

© 2002, Juan C. Martinez Cruzado 
KACIKE: The Journal of Caribbean Amerindian History and Anthropology 
ISSN 1562-5028 - 

Dr. Juan C. Martinez Cruzado - The Use of Mitochondrial DNA 

spread out more than the other, which 
suggests that shortly after the migratory 
wave to Puerto Rico, one dominated the 
other. Associated with this large group 
are two haplotypes representing only one 
sample that is separated from its nearest 
haplotypes by three mutations in one 
case and by six in the other. These ought 
to represent post-Columbian migrations 
to Puerto Rico. Finally, separated by four 
mutations from the previous group, we 
have a second group with a level of 
complexity barely greater than that of the 
AM79 of haplogroup C. Nonetheless, the 
smaller size of the central haplotype of 
this group relative to its derivatives 
suggests that it did not enjoy the 
population expansion that AM79 enjoyed 
after its arrival in Puerto Rico; the smaller 
relative size also increases its estimated 
age. We could not conclude at present if 
this second group belonged to a younger 
ceramic migration or to a relatively recent 
archaic migration. 

During this coming week, we hope 
to collect samples in the Dominican 
Republic with the intention of constructing 
median networks of the distinct 
indigenous haplogroups that we find here. 
As of this date, we can only say that we 
are lucky to have had a Dominican 
brother who passed through our 
laboratory and gave us a sample of his 

hair roots, which ended up belonging to 
haplogroup A. The sequence of bases of 
the hypervariable regions are closely 
linked but different than one of the 
hypothetical founders from the first 
migratory wave to Puerto Rico. That is to 
say that there is a relation with the 
haplotypes of Puerto Rico, but not as 
narrow as we had hoped. Of course, it is 
not possible to arrive at conclusions for 
an entire population on the basis of one 
sole sample. 

Our expectations for the 
Dominican Republic and the hypotheses 
on which they are based are the 
following. The first is simple. Hispaniola 
is much bigger and with a larger quantity 
of natural exploitable resources than 
Puerto Rico. The second is that the 
archaic Indians appear to have originated 
in Yucatan or Florida, therefore they 
would have colonized Hispaniola before 
they colonized Puerto Rico. On the other 
hand, the ceramic culture arrived in 
Puerto Rico before Hispaniola. If it is true 
that the archaic Indians of the Caribbean 
are represented by haplogroup A and, 
within haplogroup C, also by haplotype 
AM79, then we hope for less frequency in 
the Dominican Republic of haplotype 
AM79 than in Puerto Rico and, on the 
other hand, a greater frequency of 
haplogroup A and the haplotype AM32. 

Here is a "footnote" to Dr. Juan Carlos Martinez Cruzado's presentation, an informal E- 
mail message that he sent us on November 17. Thanks, Doctor, for permission to 
publish it! In the message, he talks about his analyses of the samples that we took in 
the three days after the conference and another quantity of samples taken by Lie. 
Arlene Alvarez, Director of the Regional Archaeological Museum of Altos de Chavon, 
assisted by Aldofo Lopez, an independent scholar from Spain: 

First of all, let me congratulate you 
for having graduated with honors as 
collectors of genetic material for posterity. 

The samples that Arlene sent are 
expanding the study very well. Thanks to 
you, we are getting a glimpse that there 

© 2002, Juan C. Martinez Cruzado 
KACIKE: The Journal of Caribbean Amerindian History and Anthropology 
ISSN 1562-5028 - 

Dr. Juan C. Martinez Cruzado - The Use of Mitochondrial DNA 


will be much to say about the 
mitochrondrial DNA of the Dominican 
Republic at the next Archaeology 

Up to this moment, we have tested 
for the types (haplogroups) A, B, C, and 
D on the 43 samples that we took while I 
was there. We have also tested for X 
(which is the only haplogroup that is 
absent in Puerto Rico) on 20 of them. 
Furthermore, we have tested the 32 
samples that Arlene sent for A. 

As an historian, Lynne is going to 
have a lot of work. It seems that the 
incidence of indigenous heredity in the 
Dominican Republic varies a lot with 
location. Something that we are 
beginning to see is that there is much 
more in the countryside than in the 
metropolis. But it is possible that in the 
countryside, also, there is substantial 
variability. The final results will give us an 
idea of which places the Tainos 
concentrated when they left the Spanish 
settlements. It's necessary to remember 
well the places where the samples were 
taken in order to be able to find the things 
like topography, vegetation, crops, and 
proximity to settled regions that these 
places have in common. Two things 
must always be kept in mind: 

1) events of the last two or three 
centuries will have partially erased 
some of the genetic footprints left 
by the Tainos, 

2) mitochrondrial DNA only detects 
the migration of women. 

There is a general consensus in 
Puerto Rico that the barrios known as 
Indieras in Maricao have the most people 
of indigenous origin in Puerto Rico. 
Nonetheless, the incidence of indigenous 
mitochrondrial DNA in Indieras is no 
greater than that of any other place in 
Puerto Rico outside of its eastern third. 

Clearly, the genetic difference between 
Indieras and the greater part of the rest of 
Puerto Rico must be rooted in paternal 
inheritance. In the places that did not 
serve as refuges for the Tainos, the men 
were genetically neutralized but not the 
women. The difference in the refuges is 
that the men could also procreate for the 
following generations. 

Until now, we have identified 15 
indigenous samples in the Dominican 
Republic, 12 of which have been A and 
only 3 of which are C. The best place up 
to this moment has been Tubagua, which 
is where we first stopped along the route 
from Los Cocos to Santiago [the 
mountain road called Ruta Turistica]. Of 
the 7 samples that we took there, 4 
turned out to be indigenous: 2 A and 2 C. 
A place that could beat Tubagua is El 
Seibo. From there we have only tested 9 
samples for A, and already 3 have given 
positive results. We still have to test for 
C. Another good place was Yasica, the 
second site where we stopped along the 
route from Los Cocos to Santiago. Of the 
7 samples that we took there, 3 have had 
positive results (2 A and 1 C). The next 
best site was Moncion. Of the 10 
samples that we took there, 3 tested as 
indigenous, all A. It could be that San 
Jose de las Matas will end up better than 
Moncion. There we have tested only for 
A so far, and 1 out of 7 was positive. 
Among the remainder of the indigenous 
samples, the only positive result we 
obtained was one from among the 10 
samples we took at Los Cocos. It was A. 
The 3 samples that Lynne took in San 
Juan de la Maguana were blanks, as 
were the 6 samples that we took in Santo 
Domingo. We also did a test for A among 
the 16 samples from La Romana, and not 
one gave a positive result. This suggests 
that large coastal cities near Santo 
Domingo have little incidence. To me, it 

© 2002, Juan C. Martinez Cruzado 
KACIKE: The Journal of Caribbean Amerindian History and Anthropology 
ISSN 1562-5028 - 

Dr. Juan C. Martinez Cruzado - The Use of Mitochondrial DNA 


nonetheless appears that Santiago de los 
Caballeros could have a much higher 

incidence. Dealing with a large city, it 
would be highly significant. 

I will keep you updated. 


Dr. Juan Carlos Martinez Cruzado, a 

Puerto Rican, is a professor in the 
Department of Biology at the University of 
Puerto Rico's Recinto University of 
Mayaguez. His method of detailed 
analysis of mitochondrial DNA is giving us 
new information about the migrations of 
indigenous peoples to the Caribbean and 
about today's Taino inheritance. 



Please cite this article as follows: 

Martinez Cruzado, Juan C. (2002). The 
Use of Mitochondrial DNA to Discover Pre- 
Columbian Migrations to the Caribbean: 
Results for Puerto Rico and Expectations 
for the Dominican Republic. KACIKE: The 
Journal of Caribbean Amerindian History 
and Anthropology [On-line Journal], 
Special Issue, Lynne Guitar, Ed. Available 
[Date of access: Day, Month, Year]. 

© 2002, Juan C. Martinez Cruzado 
KACIKE: The Journal of Caribbean Amerindian History and Anthropology 
ISSN 1562-5028 -